Transcriptomic profiles of rainbow trout (Oncorhynchus mykiss) selectively bred for high and low fillet yield

Authors: MANKIEWICZ, JAMIE - North Carolina State University; Gao, Guangtu; Leeds, Timothy; Cleveland, Beth

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2025
Publication Date: 6/25/2025
Citation: Mankiewicz, J., Gao, G., Leeds, T.D., Cleveland, B.M. 2025. Transcriptomic profiles of rainbow trout (Oncorhynchus mykiss) selectively bred for high and low fillet yield. Marine Biotechnology. 27. Article 102. https://doi.org/10.1007/s10126-025-10479-0.
DOI: https://doi.org/10.1007/s10126-025-10479-0

Interpretive Summary: Fillet yield is an economically important trait, especially in fish raised for food. Through breeding, the USDA National Center for Cool and Cold Water Aquaculture has produced a line of rainbow trout with high fillet yield. To understand the physiology behind this trait, gene expression profiles were analyzed in muscle and liver from these fish. Findings indicate that muscle cells proliferate more and grow larger in high fillet yield trout, and the muscle produces energy more efficiently compared to a line of trout with low fillet yield. Additionally, gene expression profiles in the liver suggest that metabolic activity in this tissue directs reduced fat deposition in high yield fish. Collectively, these findings improve our knowledge of physiological and metabolic regulation of the fillet yield trait and contribute to development of strategies to enhance fish performance.

Technical Abstract: The fillet yield phenotype is a trait that can be improved in aquaculture species through conventional selective breeding. This approach was applied to rainbow trout for three consecutive generations of selection to produce a High Yield line (HY) that exhibits 2.5 percentage points higher fillet yield compared to a Low Yield line (LY). To characterize the genetic and physiological mechanisms contributing the HY phenotype, transcriptomic analysis of liver and skeletal muscle was performed at three stages of development: 2 g, 60 g, and 300 g, which corresponded to 35-, 208-, and 277-days post hatch. Functional analysis of differentially expressed genes (DEG) suggests that increased muscle yield in the HY line is partially driven by greater hyperplasia at 60 g, although higher rates of protein accretion, primarily attributed to lower rates of protein degradation, promote muscle cell hypertrophy during all stages of development. Additionally, DEGs support reductions in glycolysis in HY muscle, with increased reliance on the more efficient citric acid cycle and oxidative phosphorylation reactions. In liver, DEGs indicate unique patterns of nutrient utilization in the HY line that support reduced visceral adiposity compared to the LY line. These findings provide insight into the physiology and metabolism driving the high fillet yield phenotype; this information is useful for the understanding of economically important production traits and support refinement of breeding strategies towards trait improvement.